TY - JOUR
T1 - MSMBuilder: Statistical Models for Biomolecular Dynamics
JF - bioRxiv
DO - 10.1101/084020
SP - 084020
AU - Harrigan, Matthew P.
AU - Sultan, Mohammad M.
AU - Hernández, Carlos X.
AU - Husic, Brooke E.
AU - Eastman, Peter
AU - Schwantes, Christian R.
AU - Beauchamp, Kyle A.
AU - McGibbon, Robert T.
AU - Pande, Vijay S.
Y1 - 2016/01/01
UR - http://biorxiv.org/content/early/2016/10/30/084020.abstract
N2 - MSMBuilder is a software package for building statistical models of high-dimensional time-series data. It is designed with a particular focus on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change. MSMBuilder is named for its ability to construct Markov State Models (MSMs), a class of models that has gained favor among computational biophysicists. In addition to both well-established and newer MSM methods, the package includes complementary algorithms for understanding time-series data such as hidden Markov models (HMMs) and time-structure based independent component analysis (tICA). MSMBuilder boasts an easy to use command-line interface, as well as clear and consistent abstractions through its Python API (application programming interface). MSMBuilder is developed with careful consideration for compatibility with the broader machine-learning community by following the design of scikit-learn. The package is used primarily by practitioners of molecular dynamics but is just as applicable to other computational or experimental time-series measurements. http://msmbuilder.org
ER -